Merge branch 'openmrs:master' into master

.github/workflows/build-2.x.yaml

@@ -28,14 +28,14 @@ jobs:
           - 8
     runs-on: ${{ matrix.platform }}
     steps:
-      - uses: actions/checkout@v2.4.0
+      - uses: actions/checkout@v3
       - name: Setup JDK
-        uses: actions/setup-java@v2
+        uses: actions/setup-java@v3
         with:
           distribution: 'adopt'
           java-version: ${{ matrix.java-version }}
       - name: Cache Maven packages
-        uses: actions/cache@v2.1.7
+        uses: actions/cache@v3
         with:
           path: ~/.m2
           key: ${{ runner.os }}-m2-${{ hashFiles('**/pom.xml') }}

.github/workflows/build.yaml

@@ -9,7 +9,7 @@ on:
       - 2.4.x
       - 2.5.x
   pull_request:
-    types: [opened, synchronize, reopened]
+    types:
     branches:
       - master
       - 2.4.x
@@ -27,20 +27,20 @@ jobs:
           - 11
     runs-on: ${{ matrix.platform }}
     steps:
-      - uses: actions/checkout@v2.4.0
+      - uses: actions/checkout@v3
       - name: Setup JDK
-        uses: actions/setup-java@v2
+        uses: actions/setup-java@v3
         with:
           distribution: 'adopt'
           java-version: ${{ matrix.java-version }}
       - name: Cache Maven packages
-        uses: actions/cache@v2.1.7
+        uses: actions/cache@v3
         with:
           path: ~/.m2
           key: ${{ runner.os }}-m2-${{ hashFiles('**/pom.xml') }}
           restore-keys: ${{ runner.os }}-m2
       - name: Cache SonarCloud packages
-        uses: actions/cache@v2.1.7
+        uses: actions/cache@v3
         with:
           path: ~/.sonar/cache
           key: ${{ runner.os }}-sonar

.github/workflows/codeql-analysis.yml

@@ -0,0 +1,70 @@
+# For most projects, this workflow file will not need changing; you simply need
+# to commit it to your repository.
+#
+# You may wish to alter this file to override the set of languages analyzed,
+# or to provide custom queries or build logic.
+#
+# ******** NOTE ********
+# We have attempted to detect the languages in your repository. Please check
+# the `language` matrix defined below to confirm you have the correct set of
+# supported CodeQL languages.
+#
+name: "CodeQL"
+
+on:
+  push:
+    branches: [ master ]
+  pull_request:
+    # The branches below must be a subset of the branches above
+    branches: [ master ]
+  schedule:
+    - cron: '45 0 * * 2'
+
+jobs:
+  analyze:
+    name: Analyze
+    runs-on: ubuntu-latest
+    permissions:
+      actions: read
+      contents: read
+      security-events: write
+
+    strategy:
+      fail-fast: false
+      matrix:
+        language: [ 'java', 'javascript' ]
+        # CodeQL supports [ 'cpp', 'csharp', 'go', 'java', 'javascript', 'python', 'ruby' ]
+        # Learn more about CodeQL language support at https://git.io/codeql-language-support
+
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v2
+
+    # Initializes the CodeQL tools for scanning.
+    - name: Initialize CodeQL
+      uses: github/codeql-action/init@v2
+      with:
+        languages: ${{ matrix.language }}
+        # If you wish to specify custom queries, you can do so here or in a config file.
+        # By default, queries listed here will override any specified in a config file.
+        # Prefix the list here with "+" to use these queries and those in the config file.
+        # queries: ./path/to/local/query, your-org/your-repo/queries@main
+
+    # Autobuild attempts to build any compiled languages  (C/C++, C#, or Java).
+    # If this step fails, then you should remove it and run the build manually (see below)
+    - name: Autobuild
+      uses: github/codeql-action/autobuild@v2
+
+    # ℹ️ Command-line programs to run using the OS shell.
+    # 📚 https://git.io/JvXDl
+
+    # ✏️ If the Autobuild fails above, remove it and uncomment the following three lines
+    #    and modify them (or add more) to build your code if your project
+    #    uses a compiled language
+
+    #- run: |
+    #   make bootstrap
+    #   make release
+
+    - name: Perform CodeQL Analysis
+      uses: github/codeql-action/analyze@v2

.github/workflows/qa.yml

@@ -8,8 +8,8 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Trigger QAFramework
-        uses: peter-evans/repository-dispatch@v1.1.3
+        uses: peter-evans/repository-dispatch@v2
         with:
           token: ${{secrets.ACTIONS_TOKEN}}
           repository: openmrs/openmrs-contrib-qaframework
-          event-type: qa-initialSetup
+          event-type: qa

.github/workflows/stale.yml

@@ -7,7 +7,7 @@ jobs:
   stale:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/stale@v4
+    - uses: actions/stale@v5
       with:
         repo-token: ${{ secrets.GITHUB_TOKEN }}
         days-before-stale: 150

api/pom.xml

@@ -178,21 +178,10 @@
 		   <groupId>org.apache.logging.log4j</groupId>
 		   <artifactId>log4j-1.2-api</artifactId>
 	   </dependency>
-	   <!-- TODO This is necessary to support Hibernate 4.x with log4j2
-	    	this dependency should be removed when upgrading Hibernate -->
-	   <dependency>
-		   <groupId>org.jboss.logging</groupId>
-		   <artifactId>jboss-logging</artifactId>
-		   <version>3.4.2.Final</version>
-	   </dependency>
 	   <dependency>
 		   <groupId>org.slf4j</groupId>
 		   <artifactId>slf4j-api</artifactId>
 	   </dependency>
-	   <dependency>
-		   <groupId>org.slf4j</groupId>
-		   <artifactId>log4j-over-slf4j</artifactId>
-	   </dependency>
 	   <dependency>
          <groupId>com.thoughtworks.xstream</groupId>
          <artifactId>xstream</artifactId>
@@ -288,6 +277,11 @@
 		   <groupId>org.apache.lucene</groupId>
 		   <artifactId>lucene-analyzers-phonetic</artifactId>
 	   </dependency>
+	   <dependency>
+		   <groupId>com.sun.mail</groupId>
+		   <artifactId>javax.mail</artifactId>
+		   <scope>test</scope>
+	   </dependency>
    </dependencies>
    <build>
      <resources>

api/src/main/java/liquibase/ext/logging/slf4j/Slf4JLogService.java

@@ -0,0 +1,36 @@
+/**
+ * This Source Code Form is subject to the terms of the Mozilla Public License,
+ * v. 2.0. If a copy of the MPL was not distributed with this file, You can
+ * obtain one at http://mozilla.org/MPL/2.0/. OpenMRS is also distributed under
+ * the terms of the Healthcare Disclaimer located at http://openmrs.org/license.
+ *
+ * Copyright (C) OpenMRS Inc. OpenMRS is a registered trademark and the OpenMRS
+ * graphic logo is a trademark of OpenMRS Inc.
+ */
+package liquibase.ext.logging.slf4j;
+
+import java.util.HashMap;
+import java.util.Map;
+
+import liquibase.logging.Logger;
+import liquibase.logging.core.AbstractLogService;
+
+/**
+ * An implementation of {@link liquibase.logging.LogService} to use SLF4J for Liquibase logging
+ * 
+ * @since 2.5.1, 2.6.0
+ */
+public class Slf4JLogService extends AbstractLogService {
+
+	private final Map<Class<?>, Slf4JLogger> loggers = new HashMap<>();
+
+	@Override
+	public int getPriority() {
+		return PRIORITY_SPECIALIZED;
+	}
+
+	@Override
+	public Logger getLog(Class clazz) {
+		return loggers.computeIfAbsent(clazz, c -> new Slf4JLogger(c, getFilter()));
+	}
+}

api/src/main/java/liquibase/ext/logging/slf4j/Slf4JLogger.java

@@ -0,0 +1,54 @@
+/**
+ * This Source Code Form is subject to the terms of the Mozilla Public License,
+ * v. 2.0. If a copy of the MPL was not distributed with this file, You can
+ * obtain one at http://mozilla.org/MPL/2.0/. OpenMRS is also distributed under
+ * the terms of the Healthcare Disclaimer located at http://openmrs.org/license.
+ *
+ * Copyright (C) OpenMRS Inc. OpenMRS is a registered trademark and the OpenMRS
+ * graphic logo is a trademark of OpenMRS Inc.
+ */
+package liquibase.ext.logging.slf4j;
+
+import java.util.logging.Level;
+
+import liquibase.logging.LogMessageFilter;
+import liquibase.logging.core.AbstractLogger;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+/**
+ * Simple layer to ensure liquibase logs get written to our standard loggers
+ * 
+ * @since 2.5.1, 2.6.0
+ */
+public class Slf4JLogger extends AbstractLogger {
+
+	private final Logger logger;
+
+	public Slf4JLogger(Class<?> clazz, LogMessageFilter filter) {
+		super(filter);
+		logger = LoggerFactory.getLogger(clazz);
+	}
+
+	@Override
+	public void log(Level level, String message, Throwable e) {
+		// NB java.util.logging supports a couple of levels not replicable through SLF4J
+		// These messages are attempted to be routed to their closest level
+
+		if (level == Level.SEVERE) {
+			logger.error(message, e);
+		} else if (level == Level.WARNING) {
+			logger.warn(message, e);
+		} else if (level == Level.INFO) {
+			logger.info(message, e);
+		} else if (level == Level.CONFIG) {
+			logger.debug(message, e);
+		} else if (level == Level.FINE) {
+			logger.debug(message, e);
+		} else if (level == Level.FINER) {
+			logger.trace(message, e);
+		} else {
+			logger.trace(message, e);
+		}
+	}
+}

api/src/main/java/org/openmrs/ConceptMapType.java

@@ -11,18 +11,31 @@
 
 import org.codehaus.jackson.annotate.JsonIgnore;
 
+import javax.persistence.Column;
+import javax.persistence.Entity;
+import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
+import javax.persistence.Id;
+import javax.persistence.Table;
+
 /**
  * ConceptMapType are used to define relationships between concepts and concept reference terms e.g
  * IS_A or SAME_AS, BROADER_THAN
  *
  * @since 1.9
  */
+@Entity
+@Table(name = "concept_map_type")
 public class ConceptMapType extends BaseChangeableOpenmrsMetadata {
-	
+
 	private static final long serialVersionUID = 1L;
-
+
+	@Id
+	@Column(name = "concept_map_type_id")
+	@GeneratedValue(strategy = GenerationType.IDENTITY)
 	private Integer conceptMapTypeId;
-
+
+	@Column(name = "is_hidden", nullable = false, length = 1)
 	private Boolean isHidden = Boolean.FALSE;
 
 	public static final String SAME_AS_MAP_TYPE_UUID = "35543629-7d8c-11e1-909d-c80aa9edcf4e";

api/src/main/java/org/openmrs/Condition.java

@@ -9,9 +9,6 @@
  */
 package org.openmrs;
 
-import java.util.Date;
-import java.util.Objects;
-
 import javax.persistence.AssociationOverride;
 import javax.persistence.AssociationOverrides;
 import javax.persistence.AttributeOverride;
@@ -29,6 +26,8 @@
 import javax.persistence.Table;
 import javax.persistence.Transient;
 
+import java.util.Date;
+
 /**
  * The condition class records detailed information about a condition, problem, diagnosis, or other
  * situation or issue. This records information about a disease/illness identified from diagnosis or
@@ -352,5 +351,5 @@ public Encounter getEncounter() {
 	public void setEncounter(Encounter encounter) {
 		this.encounter = encounter;
 	}
-			
+
 }

api/src/main/java/org/openmrs/ConditionClinicalStatus.java

@@ -38,6 +38,34 @@ public enum ConditionClinicalStatus {
 	 * the common OpenMRS use case.
 	 * Remission is where the patient is no longer experiencing the symptoms of the condition, 
 	 * but there is a risk of the symptoms returning.
+	 * 
+	 * @deprecated as of 2.6.0
 	 * */
-	HISTORY_OF 
+	HISTORY_OF,
+
+	/**
+	 * The Patient is experiencing a re-occurrence or repeating of a previously resolved condition, 
+	 * e.g. urinary tract infection, pancreatitis, cholangitis, conjunctivitis.
+	 */
+	RECURRENCE,
+
+	/**
+	 * The Patient is experiencing a return of a condition, or signs and symptoms after a period of 
+	 * improvement or remission, e.g. relapse of cancer, multiple sclerosis, rheumatoid arthritis, 
+	 * systemic lupus erythematosus, bipolar disorder, [psychotic relapse of] schizophrenia, etc.
+	 */
+	RELAPSE,
+
+	/**
+	 * The Patient is no longer experiencing the symptoms of the condition, but there is a risk 
+	 * of the symptoms returning.
+	 */
+	REMISSION,
+
+	/**
+	 * The Patient is no longer experiencing the symptoms of the condition and there is a 
+	 * negligible perceived risk of the symptoms returning.
+	 */
+	RESOLVED
+
 }